Open science

Open Science + Reproducibility

Packages

library(palmerpenguins) # penguins
library(quarto) # qmd 
library(rmarkdown) # markdown
library(tidyverse) # data wrangling

install.packages('tinytex') # for use with pdf 
tinytex::install_tinytex()
# to uninstall TinyTeX, run tinytex::uninstall_tinytex()

• You should also have Zotero installed along with Better BibTeX (nice, but not necessary)

Typical workflow

1. Do your analyses
2. Open a program (Word)
3. Copy-paste results and figures/tables
4. Manually format your results and citations

Word

Inside

Word issues

What do we want?

• Combine narrative with code (literate programming)

• Automatically generate figures and tables

• Automatically render results in text

• Format the content into a scientific paper (including citations!)

• Something that looks pretty!

• Rinse & repeat

Hello Quarto!

Hello Quarto!

• Websites (https://www.drjasongeller.com)

• Blogs

• Books (https://jgeller112.github.io/dis_flu_modeling/)

• Want to guess how I created these slides?

Big universe

• RMarkdown for EVERYONE

What is a Quarto?

How Quarto Works

Quarto handles literate programming by using a series of programs:

How Quarto Works (Source)

• knitr executes all code chunks and creates a new markdown (.md) file
• pandoc takes the markdown file generated and converts it to the desired format.
• Render inside of RStudio handles the interaction.

Advantages

(1) Eliminate/reduce human error

We found that half of all published psychology papers that use null-hypothesis significance testing (NHST) contained at least one p-value that was inconsistent with its test statistic and degrees of freedom. One in eight papers contained a grossly inconsistent p-value that may have affected the statistical conclusion)

Nuijten et al., 2016

https://michelenuijten.shinyapps.io/statcheck-web/

Advantages

(2) Easy revisions and specification of desired figures and tables

When revisions are requested, one might have to tweak tables and figures by hand constantly, leading to a major incentive never to rerun analyses because it would mean re-pasting and re-illustrating all the numbers and figures in a paper.

Advantages

(3) Promote computational reproducibility

• Easy verification and reproducilbility of research findings

• While programming environments may seem counter-intuitive for writing papers, they ultimately prevent mistakes and save time.

Create a Quarto Document

Source vs. Visual Mode

Annotated Quarto Document

Annotated sections of the “Hello Quarto” document related to document information, text formatting, and code execution

Output of a Quarto Document

Annotated source to output of the “Hello Quarto” document

Navigating a Quarto Document

Annotated “Hello Quarto” document navigation options

Metadata & Header (YAML)

• The YAML header cotains basic metadata and rendering instructions

---
title: My Reproducible Manuscript
authors:
  - name: Norah Jones
    affiliation: The University
    roles: writing
    corresponding: true
bibliography: references.bib
format: html
---

• Wait… what’s the YAML acronym?

  • Originally: “Yet Another Markup Language”

  • Later: “YAML Ain’t Markup Language”

• Set global manuscript options with key-value pairs

Code

```{r}
#| eval: true
1 + 1
```

[1] 2

Text

Section

This is a simple placeholder for the manuscript's main document [@knuth84].